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EmanuelGoncalves / crispy

Python module to analyse CRISPR-based libraries
BSD 3-Clause "New" or "Revised" License
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/mnt/efs/home/stb3865/software/anaconda3/lib/python3.8/site-packages/crispy/data/crispr_manifests//project_score_all_qc_failed_samples.csv does not exist #3

Closed laulabbumc closed 3 years ago

laulabbumc commented 3 years ago

Dear Dr. Gonçalves,

I am trying to run the following second test in the README.md file:

from crispy.CRISPRData import Library

Master Library, standardised assembly of KosukeYusa V1.1, Avana, Brunello and TKOv3

CRISPR-Cas9 libraries.

master_lib = Library.load_library("MasterLib_v1.csv.gz")

Genome-wide minimal CRISPR-Cas9 library.

minimal_lib = Library.load_library("MinLibCas9.csv.gz")

Some of the most broadly adopted CRISPR-Cas9 libraries:

'Avana_v1.csv.gz', 'Brunello_v1.csv.gz', 'GeCKO_v2.csv.gz', 'Manjunath_Wu_v1.csv.gz',

'TKOv3.csv.gz', 'Yusa_v1.1.csv.gz'

brunello_lib = Library.load_library("Brunello_v1.csv.gz")

from crispy.GuideSelection import GuideSelection

sgRNA selection class

gselection = GuideSelection()

Select 5 optimal sgRNAs for MCL1 across multiple libraries

gene_guides = gselection.select_sgrnas( "MCL1", n_guides=5, offtarget=[1, 0], jacks_thres=1, ruleset2_thres=.4 )

Perform different rounds of sgRNA selection with increasingly relaxed efficiency thresholds

gene_guides = gselection.selection_rounds("TRIM49", n_guides=5, do_amber_round=True, do_red_round=True)

import crispy as cy import matplotlib.pyplot as plt

Import data

rawcounts, copynumber = cy.Utils.get_example_data()

Import CRISPR-Cas9 library

lib = cy.Utils.get_crispr_lib()

Instantiate Crispy

crispy = cy.Crispy( raw_counts=rawcounts, copy_number=copynumber, library=lib )

Fold-changes and correction integrated funciton.

Output is a modified/expanded BED formated data-frame with sgRNA and segments information

bed_df = crispy.correct(x_features='ratio', y_feature='fold_change') print(bed_df.head())

Gaussian Process Regression is stored

crispy.gpr.plot(x_feature='ratio', y_feature='fold_change') plt.show()

When I run it,

python -m pdb test.py /mnt/efs/home/stb3865/software/crispy/test/test.py(2)() -> from crispy.CRISPRData import Library (Pdb) n /mnt/efs/home/stb3865/software/anaconda3/lib/python3.8/site-packages/sklearn/utils/deprecation.py:143: FutureWarning: The sklearn.metrics.ranking module is deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.metrics. Anything that cannot be imported from sklearn.metrics is now part of the private API. warnings.warn(message, FutureWarning) FileNotFoundError: [Errno 2] File /mnt/efs/home/stb3865/software/anaconda3/lib/python3.8/site-packages/crispy/data/crispr_manifests//project_score_all_qc_failed_samples.csv does not exist: '/mnt/efs/home/stb3865/software/anaconda3/lib/python3.8/site-packages/crispy/data/crispr_manifests//project_score_all_qc_failed_samples.csv' /mnt/efs/home/stb3865/software/crispy/test/test.py(2)() -> from crispy.CRISPRData import Library

I says "FileNotFoundError: [Errno 2] File /mnt/efs/home/stb3865/software/anaconda3/lib/python3.8/site-packages/crispy/data/crispr_manifests//project_score_all_qc_failed_samples.csv does not exist: ".

Could you please upload the missing files into github ?

Thanks!